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Lai Z, Yuan X, Chen H, Zhu Y, Dong N, Shan A. Strategies employed in the design of antimicrobial peptides with enhanced proteolytic stability. Biotechnol Adv 2022; 59:107962. [PMID: 35452776 DOI: 10.1016/j.biotechadv.2022.107962] [Citation(s) in RCA: 52] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 03/14/2022] [Accepted: 04/13/2022] [Indexed: 12/12/2022]
Abstract
Due to the alarming developing rate of multidrug-resistant bacterial pathogens, the development and modification of antimicrobial peptides (AMPs) are unprecedentedly active. Despite the fact that considerable efforts have been expended on the discovery and design strategies of AMPs, the clinical translation of peptide antibiotics remains inadequate. A large number of articles and reviews credited the limited success of AMPs to their poor stability in the biological environment, particularly their poor proteolytic stability. In the past forty years, various design strategies have been used to improve the proteolytic stability of AMPs, such as sequence modification, cyclization, peptidomimetics, and nanotechnology. Herein, we focus our discussion on the progress made in improving the proteolytic stability of AMPs and the principle, successes, and limitations of various anti-proteolytic design strategies. It is of prospective significance to extend current insights into the degradation-related inactivation of AMPs and also alleviate/overcome the problem.
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Affiliation(s)
- Zhenheng Lai
- Institute of Animal Nutrition, Northeast Agricultural University, Harbin 150030, China
| | - Xiaojie Yuan
- Institute of Animal Nutrition, Northeast Agricultural University, Harbin 150030, China
| | - Hongyu Chen
- Institute of Animal Nutrition, Northeast Agricultural University, Harbin 150030, China
| | - Yunhui Zhu
- Institute of Animal Nutrition, Northeast Agricultural University, Harbin 150030, China
| | - Na Dong
- Institute of Animal Nutrition, Northeast Agricultural University, Harbin 150030, China
| | - Anshan Shan
- Institute of Animal Nutrition, Northeast Agricultural University, Harbin 150030, China.
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2
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Shukla SP, Cho KB, Rustagi V, Gao X, Fu X, Zhang SX, Guo B, Udugamasooriya DG. "Molecular Masks" for ACE2 to Effectively and Safely Block SARS-CoV-2 Virus Entry. Int J Mol Sci 2021; 22:ijms22168963. [PMID: 34445669 PMCID: PMC8396575 DOI: 10.3390/ijms22168963] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 08/14/2021] [Accepted: 08/17/2021] [Indexed: 01/14/2023] Open
Abstract
Coronavirus Disease 2019 (COVID-19) remains a global health crisis, despite the development and success of vaccines in certain countries. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the virus that causes COVID-19, uses its spike protein to bind to the human cell surface receptor angiotensin-converting enzyme 2 (ACE2), which allows the virus to enter the human body. Using our unique cell screening technology, we identified two ACE2-binding peptoid compounds and developed dimeric derivatives (ACE2P1D1 and ACE2P2D1) that effectively blocked spike protein-ACE2 interaction, resulting in the inhibition of SARS-CoV-2 pseudovirus entry into human cells. ACE2P1D1 and ACE2P2D1 also blocked infection by a D614G mutant pseudovirus. More importantly, these compounds do not decrease ACE2 expression nor its enzyme activity (which is important in normal blood pressure regulation), suggesting safe applicability in humans
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Affiliation(s)
- Satya Prakash Shukla
- Department of Pharmacological & Pharmaceutical Sciences, University of Houston, 4849 Calhoun Rd, Houston, TX 77204-5037, USA; (S.P.S.); (K.B.C.); (V.R.); (X.G.)
| | - Kwang Bog Cho
- Department of Pharmacological & Pharmaceutical Sciences, University of Houston, 4849 Calhoun Rd, Houston, TX 77204-5037, USA; (S.P.S.); (K.B.C.); (V.R.); (X.G.)
| | - Vineeta Rustagi
- Department of Pharmacological & Pharmaceutical Sciences, University of Houston, 4849 Calhoun Rd, Houston, TX 77204-5037, USA; (S.P.S.); (K.B.C.); (V.R.); (X.G.)
| | - Xiang Gao
- Department of Pharmacological & Pharmaceutical Sciences, University of Houston, 4849 Calhoun Rd, Houston, TX 77204-5037, USA; (S.P.S.); (K.B.C.); (V.R.); (X.G.)
| | - Xinping Fu
- Department of Biology and Biochemistry, University of Houston, 3455 Cullen Blvd, Houston, TX 77204-5037, USA; (X.F.); (S.X.Z.)
| | - Shaun Xiaoliu Zhang
- Department of Biology and Biochemistry, University of Houston, 3455 Cullen Blvd, Houston, TX 77204-5037, USA; (X.F.); (S.X.Z.)
| | - Bin Guo
- Department of Pharmacological & Pharmaceutical Sciences, University of Houston, 4849 Calhoun Rd, Houston, TX 77204-5037, USA; (S.P.S.); (K.B.C.); (V.R.); (X.G.)
- Correspondence: (B.G.); (D.G.U.)
| | - D. Gomika Udugamasooriya
- Department of Pharmacological & Pharmaceutical Sciences, University of Houston, 4849 Calhoun Rd, Houston, TX 77204-5037, USA; (S.P.S.); (K.B.C.); (V.R.); (X.G.)
- MD Anderson Cancer Center, Department of Cancer Systems Imaging, 1881 East Road, Houston, TX 77030-4009, USA
- Correspondence: (B.G.); (D.G.U.)
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Lyu D, Shi Y, Lyu X. Effect of antiamyloid-β drugs on Alzheimer's disease: study protocol for a systematic review and meta-analysis. BMJ Open 2021; 11:e048453. [PMID: 34006557 PMCID: PMC8137253 DOI: 10.1136/bmjopen-2020-048453] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
INTRODUCTION Alzheimer's disease (AD) is a neurodegenerative disease with a complex aetiology involving multiple targets and pathways. With the continuous growth of the ageing population, the burden of AD is increasing year by year. However, there has not been new drug approved for over a decade. In addition, the efficacy of memantine and cholinesterase inhibitors is not satisfactory. As amyloid-β (Aβ) is regarded as the core pathological change and the trigger mechanism of AD, anti-Aβ therapy may be an effective therapy. In recent years, a lot of clinical trials have been carried out in this field, but the results have not been well summarised and analysed. METHODS AND ANALYSIS In this study, we will study the effect of anti-Aβ antibodies versus placebo on the clinical efficacy, biomarkers, neuroimaging and safety in different stages of AD, as well as the factors that may affect the efficacy. Drugs that only target the existing Aβ are regarded as anti-Aβ antibodies. Following electronic databases will be searched from inception to April 2021: Medline-Ovid, EMBase-Ovid, Cochrane Central and clinical trial registration platform ClinicalTrials.gov. After identifying eligible studies through screening title, abstract and read full text of each retrieved literature, we will contact the correspondence authors for additional information and grey literatures. To get more reliable results, random effect model will be conducted for meta-analysis and analysis of subgroups or subsets. Funnel plot, Egger's test and sensitivity analysis will be conducted to explore potential heterogeneity. Meta-regression will be conducted to identify the factors that may affect clinical efficacy. Evidence quality assessment and trial sequential analysis will be conducted to assess the quality of evidence and confirm the reliability of the results in this study. ETHICS AND DISCUSSION This study does not require formal ethical approval. The findings will be submitted to a peer-review journal. PROSPERO REGISTRATION NUMBER CRD42020202370.
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Affiliation(s)
- Diyang Lyu
- Capital Medical University, Beijing, China
| | - Yuqing Shi
- Capital Medical University, Beijing, China
| | - Xuanxin Lyu
- Neurological Rehabilitation Center, Beijing Rehabilitation Hospital, Capital Medical University, Beijing, China
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Liu S, Dang M, Lei Y, Ahmad SS, Khalid M, Kamal MA, Chen L. Ajmalicine and its Analogues Against AChE and BuChE for the Management of Alzheimer's Disease: An In-silico Study. Curr Pharm Des 2021; 26:4808-4814. [PMID: 32264807 DOI: 10.2174/1381612826666200407161842] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Accepted: 03/02/2020] [Indexed: 01/29/2023]
Abstract
BACKGROUND Alzheimer's disease (AD) is the most well-known reason for disability in persons aged greater than 65 years worldwide. AD influences the part of the brain that controls cognitive and non-cognitive functions. OBJECTIVE The study focuses on the screening of natural compounds for the inhibition of AChE and BuChE using a computational methodology. METHODS We performed a docking-based virtual screening utilizing the 3D structure of AChE and BuChE to search for potential inhibitors for AD. In this work, a screened inhibitor Ajmalicine similarity search was carried out against a natural products database (Super Natural II). Lipinski rule of five was carried out and docking studies were performed between ligands and enzyme using 'Autodock4.2'. RESULTS Two phytochemical compounds SN00288228 and SN00226692 were predicted for the inhibition of AChE and BuChE, respectively. The docking results revealed Ajmalicine, a prominent natural alkaloid, showing promising inhibitory potential against AChE and BuChE with the binding energy of -9.02 and -8.89 kcal/mole, respectively. However, SN00288228- AChE, and SN00226692-BuChE were found to have binding energy -9.88 and -9.54 kcal/mole, respectively. These selected phytochemical compounds showed better interactions in comparison to Ajmalicine with the target molecule. CONCLUSION The current study verifies that SN00288228 and SN00226692 are more capable inhibitors of human AChE and BuChE as compared to Ajmalicine with reference to ΔG values.
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Affiliation(s)
- Shu Liu
- Department of Neurology, Tangshan Workers Hospital, Tangshan, Hebei, 063000, China
| | - Minyan Dang
- Innoscience Research Sdn Bhd, Jalan USJ 25/1, 47650 Subang Jaya, Selangor, Malaysia
| | - Yan Lei
- Innoscience Research Sdn Bhd, Jalan USJ 25/1, 47650 Subang Jaya, Selangor, Malaysia
| | - Syed S Ahmad
- Department of Bioengineering, Faculty of Engineering, Integral University, Lucknow, India
| | - Mohammad Khalid
- Department of Pharmacognosy, College of Pharmacy, Prince Sattam Bin Abdulaziz University, P.O. Box 173, Al-Kharj 11942, Saudi Arabia
| | - Mohammad A Kamal
- King Fahd Medical Research Center, King Abdulaziz University, P.O. Box 80216, Jeddah 21589, Kingdom of Saudi Arabia,Enzymoics; Novel Global Community Educational Foundation, 7 Peterlee Place, Hebersham, NSW 2770,
Australia
| | - Li Chen
- Department of Neurology, Shaanxi Provincial People’s Hospital, 256 friendship west road, BinLin, Xi’an, Shaanxi,
710068, China
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Wątły J, Miller A, Kozłowski H, Rowińska-Żyrek M. Peptidomimetics - An infinite reservoir of metal binding motifs in metabolically stable and biologically active molecules. J Inorg Biochem 2021; 217:111386. [PMID: 33610030 DOI: 10.1016/j.jinorgbio.2021.111386] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2020] [Revised: 01/14/2021] [Accepted: 01/27/2021] [Indexed: 12/12/2022]
Abstract
The involvement of metal ions in interactions with therapeutic peptides is inevitable. They are one of the factors able to fine-tune the biological properties of antimicrobial peptides, a promising group of drugs with one large drawback - a problematic metabolic stability. Appropriately chosen, proteolytically stable peptidomimetics seem to be a reasonable solution of the problem, and the use of D-, β-, γ-amino acids, unnatural amino acids, azapeptides, peptoids, cyclopeptides and dehydropeptides is an infinite reservoir of metal binding motifs in metabolically stable, well-designed, biologically active molecules. Below, their specific structural features, metal-chelating abilities and antimicrobial potential are discussed.
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Affiliation(s)
- Joanna Wątły
- Faculty of Chemistry, University of Wroclaw, Joliot - Curie 14, Wroclaw 50-383, Poland.
| | - Adriana Miller
- Faculty of Chemistry, University of Wroclaw, Joliot - Curie 14, Wroclaw 50-383, Poland
| | - Henryk Kozłowski
- Faculty of Chemistry, University of Wroclaw, Joliot - Curie 14, Wroclaw 50-383, Poland; Department of Health Sciences, University of Opole, Katowicka 68, Opole 45-060, Poland
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Xuan S, Zuckermann RN. Engineering the atomic structure of sequence-defined peptoid polymers and their assemblies. POLYMER 2020. [DOI: 10.1016/j.polymer.2020.122691] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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Solid-Phase Insertion of N-mercaptoalkylglycine Residues into Peptides. Molecules 2019; 24:molecules24234261. [PMID: 31766740 PMCID: PMC6930625 DOI: 10.3390/molecules24234261] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Revised: 11/18/2019] [Accepted: 11/20/2019] [Indexed: 11/18/2022] Open
Abstract
N-mercaptoalkylglycine residues were inserted into peptides by reacting N-free amino groups of peptides, which were initially synthesized on 2-chlorotrityl resin (Cltr) using the Fmoc/tBu method, with bromoacetic acid and subsequent nucleophilic replacement of the bromide by reacting with S-4-methoxytrityl- (Mmt)/S-trityl- (Trt) protected aminothiols. The synthesized thiols containing peptide–peptoid hybrids were cleaved from the resin, either protected by treatment with dichloromethane (DCM)/trifluoroethanol (TFE)/acetic acid (AcOH) (7:2:1), or deprotected (fully or partially) by treatment with trifluoroacetic acid (TFA) solution using triethylsilane (TES) as a scavenger.
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Andreev K, Martynowycz MW, Gidalevitz D. Peptoid drug discovery and optimization via surface X-ray scattering. Biopolymers 2019; 110:e23274. [PMID: 30892696 PMCID: PMC6661014 DOI: 10.1002/bip.23274] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2018] [Revised: 03/01/2019] [Accepted: 03/04/2019] [Indexed: 12/31/2022]
Abstract
Synthetic polymers mimicking antimicrobial peptides have drawn considerable interest as potential therapeutics. N-substituted glycines, or peptoids, are recognized by their in vivo stability and ease of synthesis. Peptoids are thought to act primarily on the negatively charged lipids that are abundant in bacterial cell membranes. A mechanistic understanding of lipid-peptoid interaction at the molecular level will provide insights for rational design and optimization of peptoids. Here, we highlight recent studies that utilize synchrotron liquid surface X-ray scattering to characterize the underlying peptoid interactions with bacterial and eukaryotic membranes. Cellular membranes are highly complex, and difficult to characterize at the molecular level. Model systems including Langmuir monolayers, are used in these studies to reduce system complexity. The general workflow of these systems and the corresponding data analysis techniques are presented alongside recent findings. These studies investigate the role of peptoid physicochemical characteristics on membrane activity. Specifically, the roles of cationic charge, conformational constraint via macrocyclization, and hydrophobicity are shown to correlate their membrane interactions to biological activities in vitro. These structure-activity relationships have led to new insights into the mechanism of action by peptoid antimicrobials, and suggest optimization strategies for future therapeutics based on peptoids.
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Affiliation(s)
- Konstantin Andreev
- Howard Hughes Medical Institute, Northwestern University, Evanston, Illinois
| | | | - David Gidalevitz
- Center for the Molecular Study of Condensed Soft Matter and Department of Physics, Illinois Institute of Technology, Chicago, Illinois
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Nguyen AI, Spencer RK, Anderson CL, Zuckermann RN. A bio-inspired approach to ligand design: folding single-chain peptoids to chelate a multimetallic cluster. Chem Sci 2018; 9:8806-8813. [PMID: 30746115 PMCID: PMC6335634 DOI: 10.1039/c8sc04240c] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Accepted: 11/05/2018] [Indexed: 12/12/2022] Open
Abstract
Synthesis of biomimetic multimetallic clusters is sought after for applications such as efficient storage of solar energy and utilization of greenhouse gases. However, synthetic efforts are hampered by a dearth of ligands that are developed for multimetallic clusters due to current limitations in rational design and organic synthesis. Peptoids, a synthetic sequence-defined oligomer, enable a biomimetic strategy to rapidly synthesize and optimize large, multifunctional ligands by structural design and combinatorial screening. Here we discover peptoid oligomers (≤7 residues) that fold into a single conformation to provide unprecedented tetra- and hexadentate chelation by carboxylates to a [Co4O4] cubane cluster. The structures of peptoid-bound cubanes were determined by 2D NMR spectroscopy, and their structures reveal key steric and side-chain-to-main chain interactions that work in concert to rigidify the peptoid ligand. This efficient ligand design strategy holds promise for creating new scaffolds for the abiotic synthesis and manipulation of multimetallic clusters.
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Affiliation(s)
- Andy I Nguyen
- Molecular Foundry , Lawrence Berkeley National Laboratory , Berkeley , CA 94720 , USA .
| | - Ryan K Spencer
- Department of Chemistry , Department of Chemical Engineering & Materials Science , University of California , Irvine , CA 92697 , USA
| | | | - Ronald N Zuckermann
- Molecular Foundry , Lawrence Berkeley National Laboratory , Berkeley , CA 94720 , USA .
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An Aβ42 variant that inhibits intra- and extracellular amyloid aggregation and enhances cell viability. Biochem J 2018; 475:3087-3103. [DOI: 10.1042/bcj20180247] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2018] [Revised: 09/02/2018] [Accepted: 09/07/2018] [Indexed: 01/06/2023]
Abstract
Aggregation and accumulation of the 42-residue amyloid β peptide (Aβ42) in the extracellular matrix and within neuronal cells is considered a major cause of neuronal cell cytotoxicity and death in Alzheimer's disease (AD) patients. Therefore, molecules that bind to Aβ42 and prevent its aggregation are therapeutically promising as AD treatment. Here, we show that a non-self-aggregating Aβ42 variant carrying two surface mutations, F19S and L34P (Aβ42DM), inhibits wild-type Aβ42 aggregation and significantly reduces Aβ42-mediated cell cytotoxicity. In addition, Aβ42DM inhibits the uptake and internalization of extracellularly added pre-formed Aβ42 aggregates into cells. This was the case in both neuronal and non-neuronal cells co-expressing Aβ42 and Aβ42DM or following pre-treatment of cells with extracellular soluble forms of the two peptides, even at high Aβ42 to Aβ42DM molar ratios. In cells, Aβ42DM associates with Aβ42, while in vitro, the two soluble recombinant peptides exhibit nano-molar binding affinity. Importantly, Aβ42DM potently suppresses Aβ42 amyloid aggregation in vitro, as demonstrated by thioflavin T fluorescence and transmission electron microscopy for detecting amyloid fibrils. Overall, we present a new approach for inhibiting Aβ42 fibril formation both within and outside cells. Accordingly, Aβ42DM should be evaluated in vivo for potential use as a therapeutic lead for treating AD.
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